The genetic PA risk factors in SNP context inherent to the Brazilian population have not been studied so far. Here we observed 9 SNPs associated with PA risk (p<0.05) with the most significantly associated being rs3790844, rs9854771, rs2941471, rs4016812, rs13303010 and rs9543325. A very important aspect in our results for these SNPs is that for all of them the OR is in the same direction of the original GWAS work.
The first SNP is located at the first intron of NR5A2, with MAF in global population of 25%, and we observed a similar value of 27% in our control group, while in PA patients this value was 18%, returning an OR that represents a protective effect of this allele for PA. In a meta-analysis by Chen et al, this SNP had a protective effect in Caucasians, although not in Asian populations[28]. However, another study with 360 pancreatic cancer patients and 400 controls suggested that this SNP is related with pancreatic cancer risk in Japanese subjects [28]. A large study using 3851 pancreatic cancer cases and 3934 controls participants from the previously conducted GWAS in the Pancreatic Cancer Cohort Consortium and the Pancreatic Cancer Case Control Consortium (PanC4)[17,18] showed this SNP as the most significant risk factor for pancreatic cancer, with an OR of 0.77 , again representing a protective effect of minor allele[29].
The SNP rs9854771 has a MAF in global population of 37%. In our control group we observed a similar MAF of 39%, while in PA cases it was 25%. This SNP is located near TP63 gene, that is a p53 homologue and implicated in tumorigenesis and metastasis[30], and previous GWAS studies have demonstrated significant evidence of association for SNPs in TP63 in lung cancer and bladder cancer [31–35] . The first description of its role in pancreatic cancer was revealed by Childs[36] with an OR of 0.89 and a subsequent study [37] returned a similar result with an OR 0.76.
A third SNP where the minor allele is associated with a reduction in PA risk is rs2941471 and its MAF in global population is 41%. Here, the control group show a MAF of 44%, while in the PA cases it is 35%. This SNP is located is an intronic region of HNF4G gene, at chromosome 8q21.11, which encodes hepatocyte nuclear factor 4 gamma, a transcription factor of the nuclear receptor superfamily whose expression level was increased in five of six clinical human hepatocellular carcinoma samples[38]. When related with pancreas, mice lacking HNF4G have higher numbers of pancreatic β-cells, increased glucose-induced insulin secretion and improved glucose tolerance[39]. A research showing GWAS pathways associated with pancreatic cancer susceptibility factors proposed a link between HNF4G inherited variation for pancreatic development[29]. A very consistent research with 2737 pancreatic cancer patients and 4752 controls also yielded this SNP as a genome-wide significant locus (OR=0.87)[22].
For SNP rs9543325, the global MAF is 38%, similar the frequency of 44% found in our control Brazilian population. In PA, this value increased to 56% and was associated with increased risk for pancreatic cancer in all models analyzed. This association was previously showed in Europeans [17,40], including Jewish and non-Jewish[41], and in the Taiwanese population [42]. This intergenic SNP maps at 13q22.1 locus, and has been showed to be strongly associated with pancreatic cancer [1,3,37,41–43]. The locus 13q22.1 has other SNPs associated previously with PA, mainly in European and Chinese populations, some studies suggest a potential long-range enhancer activity but mechanisms are still unknown [44].
The SNP rs13303010 has a global population MAF of 12%. In our control group this value was increased to 22% and, among PA patients this frequency increased to 37% and was associated with high cancer risk. The minor allele was also associated with increased PA risk in European [22] and Japanese populations [45]. In European populations, it was highlighted in PA susceptibility only in the largest pancreatic cancer GWAS to date, including 11,537 patients and 17,107 controls from the Pancreatic Cancer Cohort Consortium (PanScan I+II, III), Pancreatic Cancer Case-Control Consortium (PanC4) and PANcreatic Disease ReseArch (PANDoRA) consortium[22]. In the Japanese population, 664 pancreatic cancer cases and 664 controls were analyzed and this SNP was highlighted as PA risk factor[45]. This SNP is mapped at 1p36.33, in the first intron of the NOC2L gene and probably influences the host expression. The presence of the risk-increasing allele was associated with higher NOC2L expression [22] and this gene encodes the NOC2 like nucleolar associated transcriptional repressor, a protein that represents a novel histone deacetylases-independent inhibitor of histone acetyltransferase [46]. NOC2-like protein has also been associated with the inhibition of p53 and p63 tumor suppressor [47,48], notably associated with cancer.
The rs401681 is a SNP located in the intron of CLPTM1L and 27 kb from the TERT gene, being associated with many tumor types [49,50]. The global population MAF is 43% and, in the Brazilian population, we found a similar frequency of 45% in the control group. In the present study, the presence of the minor allele represents a risk factor for pancreatic cancer. This high risk for PA was also shown in European [18,40,51] and Asian populations [52,53]. It is suggested that rs401681 confers cancer susceptibility by regulating CLPTM1L and TERT expression [54], both genes implicated in carcinogenesis. CLPTM1L gene may be associated in apoptosis processes and high expressed in cisplatin-resistant cell lines [55], TERT gene produce catalytic subunit of telomerase, associated with telomere maintaining and usually active in cancer cells [56]. An interesting aspect in rs401681 is that the minor allele is usually associated with increased risk in pancreatic cancer and in melanoma [57] whereas the C allele was associated with increased risk of other tumor types, such as lung, prostate and bladder [49].
Some other SNPs showed statistically significant associations with PA risk in this work. The minor allele of rs17688601, in SUGCT gene, and rs4795218, in HNF1B gene, were associated with reduced risk in the European population [22,36]. In the Brazilian population we found them also associated with protection, but only in allelic model. On the other hand, another SNP previously associated SNP in Europeans, the rs7310409 in HNF1A, was associated with risk in dominant and co-dominant models, but not in allelic analysis (P=0.065). The other SNPs analyzed were not associated with PA in the Brazilian population in the present study.